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Check your WSI client settings. When something has timmed out for me it has been the client timeout setings more than the server. Which gets down to adding some settings to a binding in the basicHttpBinding section.

Just because the server changed it doesn't mean that client changes are not needed either. Since responses can now be taking longer than what the client is used to. You can apply the binding settings the server 1st if you so desire.

Eventually I re-wrote the SP. It was taking about 50 seconds and I got it down to 19. But I wasn't happy with that, so I wrote another sp which prepared the data into a new table about a minute before it was needed on a sql agent job. Then along comes the original sp which is called from one of our other sites to grab the data, which takes less than a second.